RAxML-NG v. 1.0.2 released on 22.02.2021 by The Exelixis Lab.
Developed by: Alexey M. Kozlov and Alexandros Stamatakis.
Contributors: Diego Darriba, Tomas Flouri, Benoit Morel, Sarah Lutteropp, Ben Bettisworth.
Latest version: https://github.com/amkozlov/raxml-ng
Questions/problems/suggestions? Please visit: https://groups.google.com/forum/#!forum/raxml

System: Intel(R) Xeon(R) Gold 6148 CPU @ 2.40GHz, 40 cores, 376 GB RAM

RAxML-NG was called at 05-Jul-2021 13:32:31 as follows:

raxml-ng --msa /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/2_msa/Q9UQ88_trimmed_msa.fasta --data-type AA --model LG4X --prefix /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88 --seed 2 --threads 6 --tree rand{20} pars{20}

Analysis options:
  run mode: ML tree search
  start tree(s): random (20)
  random seed: 2
  tip-inner: OFF
  pattern compression: ON
  per-rate scalers: OFF
  site repeats: ON
  fast spr radius: AUTO
  spr subtree cutoff: 1.000000
  branch lengths: proportional (ML estimate, algorithm: NR-FAST)
  SIMD kernels: AVX2
  parallelization: coarse-grained (auto), PTHREADS (6 threads), thread pinning: OFF

[00:00:00] Reading alignment from file: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/2_msa/Q9UQ88_trimmed_msa.fasta
[00:00:00] Loaded alignment with 1001 taxa and 368 sites

WARNING: Sequences tr_A0A1D5NZU4_A0A1D5NZU4_CHICK_9031 and tr_H0YXV7_H0YXV7_TAEGU_59729 are exactly identical!
WARNING: Sequences tr_A0A1D5NZU4_A0A1D5NZU4_CHICK_9031 and tr_U3K436_U3K436_FICAL_59894 are exactly identical!
WARNING: Sequences tr_A0A1D5NZU4_A0A1D5NZU4_CHICK_9031 and tr_U3IX19_U3IX19_ANAPL_8839 are exactly identical!
WARNING: Sequences tr_A0A1D5NZU4_A0A1D5NZU4_CHICK_9031 and tr_A0A091F7J3_A0A091F7J3_CORBR_85066 are exactly identical!
WARNING: Sequences tr_A0A1D5NZU4_A0A1D5NZU4_CHICK_9031 and tr_A0A093Q146_A0A093Q146_9PASS_328815 are exactly identical!
WARNING: Sequences tr_A0A1D5NZU4_A0A1D5NZU4_CHICK_9031 and tr_A0A091UTL1_A0A091UTL1_NIPNI_128390 are exactly identical!
WARNING: Sequences tr_A0A1D5NZU4_A0A1D5NZU4_CHICK_9031 and tr_A0A0A0AV83_A0A0A0AV83_CHAVO_50402 are exactly identical!
WARNING: Sequences tr_A0A1D5NZU4_A0A1D5NZU4_CHICK_9031 and tr_A0A091ILX5_A0A091ILX5_CALAN_9244 are exactly identical!
WARNING: Sequences tr_A0A1D5NZU4_A0A1D5NZU4_CHICK_9031 and tr_A0A1V4KNM4_A0A1V4KNM4_PATFA_372326 are exactly identical!
WARNING: Sequences tr_A0A1D5NZU4_A0A1D5NZU4_CHICK_9031 and tr_A0A226PFH8_A0A226PFH8_COLVI_9014 are exactly identical!
WARNING: Sequences tr_J3K4B2_J3K4B2_COCIM_246410 and tr_A0A0J6YGP0_A0A0J6YGP0_COCIT_404692 are exactly identical!
WARNING: Sequences tr_B6QDC6_B6QDC6_TALMQ_441960 and tr_A0A093VZ60_A0A093VZ60_TALMA_1077442 are exactly identical!
WARNING: Sequences tr_Q290T0_Q290T0_DROPS_46245 and tr_B4GBA4_B4GBA4_DROPE_7234 are exactly identical!
WARNING: Sequences tr_A0A2I3T1A1_A0A2I3T1A1_PANTR_9598 and sp_P21127_CD11B_HUMAN_9606 are exactly identical!
WARNING: Sequences tr_F9GBP1_F9GBP1_FUSOF_660025 and tr_N4USL9_N4USL9_FUSC1_1229664 are exactly identical!
WARNING: Sequences tr_F9GBP1_F9GBP1_FUSOF_660025 and tr_X0DKB7_X0DKB7_FUSOX_1089458 are exactly identical!
WARNING: Sequences tr_A0A088ATD3_A0A088ATD3_APIME_7460 and tr_A0A2A3EIH3_A0A2A3EIH3_APICC_94128 are exactly identical!
WARNING: Sequences sp_Q15131_CDK10_HUMAN_9606 and tr_A0A2R9A3I8_A0A2R9A3I8_PANPA_9597 are exactly identical!
WARNING: Sequences tr_J3LZ34_J3LZ34_ORYBR_4533 and tr_A0A0E0H2D9_A0A0E0H2D9_ORYNI_4536 are exactly identical!
WARNING: Sequences tr_J3LZ34_J3LZ34_ORYBR_4533 and sp_A2XUW1_CDKG2_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_J3LZ34_J3LZ34_ORYBR_4533 and tr_A0A0E0PAT8_A0A0E0PAT8_ORYRU_4529 are exactly identical!
WARNING: Sequences tr_J3LZ34_J3LZ34_ORYBR_4533 and tr_A0A0D9ZMF4_A0A0D9ZMF4_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_J3LZ34_J3LZ34_ORYBR_4533 and tr_A0A0E0KS44_A0A0E0KS44_ORYPU_4537 are exactly identical!
WARNING: Sequences tr_J3LZ34_J3LZ34_ORYBR_4533 and sp_Q7XUF4_CDKG2_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_A0A0E0G9J5_A0A0E0G9J5_ORYNI_4536 and sp_A2X6X1_CDKG1_ORYSI_39946 are exactly identical!
WARNING: Sequences tr_G7XD11_G7XD11_ASPKW_1033177 and tr_A0A146FEG1_A0A146FEG1_9EURO_1069201 are exactly identical!
WARNING: Sequences tr_W4XRM5_W4XRM5_STRPU_7668 and tr_W4ZDS7_W4ZDS7_STRPU_7668 are exactly identical!
WARNING: Sequences tr_F4PAM0_F4PAM0_BATDJ_684364 and tr_A0A177WUI0_A0A177WUI0_BATDE_403673 are exactly identical!
WARNING: Sequences tr_I1P1Y4_I1P1Y4_ORYGL_4538 and tr_A0A0D3F7A1_A0A0D3F7A1_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_I1P1Y4_I1P1Y4_ORYGL_4538 and tr_A0A0D9YUK7_A0A0D9YUK7_9ORYZ_40148 are exactly identical!
WARNING: Sequences tr_I1P1Y4_I1P1Y4_ORYGL_4538 and sp_Q6K5F8_CDKG1_ORYSJ_39947 are exactly identical!
WARNING: Sequences tr_I1PMG9_I1PMG9_ORYGL_4538 and tr_A0A0D3FXA7_A0A0D3FXA7_9ORYZ_65489 are exactly identical!
WARNING: Sequences tr_F4W888_F4W888_ACREC_103372 and tr_A0A151HYR3_A0A151HYR3_9HYME_520822 are exactly identical!
WARNING: Sequences tr_F4X4W7_F4X4W7_ACREC_103372 and tr_A0A151WL98_A0A151WL98_9HYME_64791 are exactly identical!
WARNING: Sequences tr_F4X4W7_F4X4W7_ACREC_103372 and tr_A0A151HYU0_A0A151HYU0_9HYME_520822 are exactly identical!
WARNING: Sequences tr_G2XWQ2_G2XWQ2_BOTF4_999810 and tr_M7TLW1_M7TLW1_BOTF1_1290391 are exactly identical!
WARNING: Sequences tr_A0A0D2XZR6_A0A0D2XZR6_FUSO4_426428 and tr_A0A2H3GK44_A0A2H3GK44_FUSOX_327505 are exactly identical!
WARNING: Sequences tr_G7Q002_G7Q002_MACFA_9541 and tr_A0A2K5YPS2_A0A2K5YPS2_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A337RTF9_A0A337RTF9_FELCA_9685 and tr_A0A2U3WFK1_A0A2U3WFK1_ODORO_9708 are exactly identical!
WARNING: Sequences tr_A0A337RTF9_A0A337RTF9_FELCA_9685 and tr_A0A384DS74_A0A384DS74_URSMA_29073 are exactly identical!
WARNING: Sequences tr_M7Z0W2_M7Z0W2_TRIUA_4572 and tr_A0A3B6NQJ9_A0A3B6NQJ9_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_V2XX61_V2XX61_MONRO_1381753 and tr_A0A0W0G2R9_A0A0W0G2R9_9AGAR_221103 are exactly identical!
WARNING: Sequences tr_A0A3B6B1Q3_A0A3B6B1Q3_WHEAT_4565 and tr_A0A3B6C8U2_A0A3B6C8U2_WHEAT_4565 are exactly identical!
WARNING: Sequences tr_A0A015M5X6_A0A015M5X6_9GLOM_1432141 and tr_A0A2H5UE38_A0A2H5UE38_RHIID_747089 are exactly identical!
WARNING: Sequences tr_A0A044R0Y9_A0A044R0Y9_ONCVO_6282 and tr_A0A182E261_A0A182E261_ONCOC_42157 are exactly identical!
WARNING: Sequences tr_A0A087X8S3_A0A087X8S3_POEFO_48698 and tr_A0A087XTA3_A0A087XTA3_POEFO_48698 are exactly identical!
WARNING: Sequences tr_A0A096MPP3_A0A096MPP3_PAPAN_9555 and tr_A0A2K5YNL9_A0A2K5YNL9_MANLE_9568 are exactly identical!
WARNING: Sequences tr_A0A2I3M6E2_A0A2I3M6E2_PAPAN_9555 and tr_A0A2K6AYT5_A0A2K6AYT5_MACNE_9545 are exactly identical!
WARNING: Sequences tr_A0A094GHX1_A0A094GHX1_9PEZI_1420912 and tr_A0A2P2SWA8_A0A2P2SWA8_9PEZI_342668 are exactly identical!
WARNING: Sequences tr_A0A0A0KQ05_A0A0A0KQ05_CUCSA_3659 and tr_A0A1S3BE56_A0A1S3BE56_CUCME_3656 are exactly identical!
WARNING: Sequences tr_V4VFQ7_V4VFQ7_9ROSI_85681 and tr_A0A2H5NV91_A0A2H5NV91_CITUN_55188 are exactly identical!
WARNING: Sequences tr_A0A0D2W0E7_A0A0D2W0E7_GOSRA_29730 and tr_A0A1U8INB9_A0A1U8INB9_GOSHI_3635 are exactly identical!
WARNING: Sequences tr_A0A0F8V5J2_A0A0F8V5J2_9EURO_308745 and tr_A0A2T5LQD0_A0A2T5LQD0_9EURO_1392256 are exactly identical!
WARNING: Sequences tr_A0A0V1CQB1_A0A0V1CQB1_TRIBR_45882 and tr_A0A0V0ZRJ2_A0A0V0ZRJ2_9BILA_990121 are exactly identical!
WARNING: Sequences tr_A0A0V1CQB1_A0A0V1CQB1_TRIBR_45882 and tr_A0A0V1NLX5_A0A0V1NLX5_9BILA_92180 are exactly identical!
WARNING: Sequences tr_A0A0V1CQB1_A0A0V1CQB1_TRIBR_45882 and tr_A0A0V0TGP1_A0A0V0TGP1_9BILA_144512 are exactly identical!
WARNING: Sequences tr_A0A100ILD2_A0A100ILD2_ASPNG_5061 and tr_A0A1L9N471_A0A1L9N471_ASPTU_767770 are exactly identical!
WARNING: Sequences tr_A0A164U5R1_A0A164U5R1_9HOMO_1314777 and tr_A0A166J5C5_A0A166J5C5_9HOMO_1314776 are exactly identical!
WARNING: Sequences tr_A0A1S4B0A9_A0A1S4B0A9_TOBAC_4097 and tr_A0A1S4CKK2_A0A1S4CKK2_TOBAC_4097 are exactly identical!
WARNING: Sequences tr_A0A1S4B0A9_A0A1S4B0A9_TOBAC_4097 and tr_A0A314KK19_A0A314KK19_NICAT_49451 are exactly identical!
WARNING: Sequences tr_A0A1U8FDF7_A0A1U8FDF7_CAPAN_4072 and tr_A0A2G3B8V1_A0A2G3B8V1_CAPCH_80379 are exactly identical!
WARNING: Duplicate sequences found: 61

NOTE: Reduced alignment (with duplicates and gap-only sites/taxa removed) 
NOTE: was saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88.raxml.reduced.phy

Alignment comprises 1 partitions and 368 patterns

Partition 0: noname
Model: LG4X+R4
Alignment sites / patterns: 368 / 368
Gaps: 5.90 %
Invariant sites: 0.54 %


NOTE: Binary MSA file created: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88.raxml.rba

Parallelization scheme autoconfig: 6 worker(s) x 1 thread(s)

Parallel reduction/worker buffer size: 1 KB  / 0 KB

[00:00:00] Generating 20 random starting tree(s) with 1001 taxa
[00:00:00] Data distribution: max. partitions/sites/weight per thread: 1 / 368 / 29440
[00:00:00] Data distribution: max. searches per worker: 4

Starting ML tree search with 20 distinct starting trees

[00:00:00 -489183.201643] Initial branch length optimization
[00:00:08 -421550.406770] Model parameter optimization (eps = 10.000000)
[00:01:05 -419359.816098] AUTODETECT spr round 1 (radius: 5)
[00:05:57 -284412.013715] AUTODETECT spr round 2 (radius: 10)
[00:10:52 -216236.384355] AUTODETECT spr round 3 (radius: 15)
[00:16:24 -180533.468292] AUTODETECT spr round 4 (radius: 20)
[00:22:14 -162315.630106] AUTODETECT spr round 5 (radius: 25)
[00:29:05 -159678.120939] SPR radius for FAST iterations: 25 (autodetect)
[00:29:05 -159678.120939] Model parameter optimization (eps = 3.000000)
[00:29:42 -159639.512132] FAST spr round 1 (radius: 25)
[00:35:40 -137030.650998] FAST spr round 2 (radius: 25)
[00:39:52 -136264.976860] FAST spr round 3 (radius: 25)
[00:43:15 -136214.598581] FAST spr round 4 (radius: 25)
[00:46:11 -136205.144181] FAST spr round 5 (radius: 25)
[00:49:06 -136203.227578] FAST spr round 6 (radius: 25)
[00:51:57 -136201.690518] FAST spr round 7 (radius: 25)
[00:54:45 -136201.690464] Model parameter optimization (eps = 1.000000)
[00:55:14 -136193.519402] SLOW spr round 1 (radius: 5)
[00:59:30 -136158.475053] SLOW spr round 2 (radius: 5)
[01:03:31 -136152.357895] SLOW spr round 3 (radius: 5)
[01:07:27 -136152.197567] SLOW spr round 4 (radius: 5)
[01:11:10 -136152.197566] SLOW spr round 5 (radius: 10)
[01:14:53 -136152.197566] SLOW spr round 6 (radius: 15)
[01:21:40 -136151.113656] SLOW spr round 7 (radius: 5)
[01:26:39 -136151.113656] SLOW spr round 8 (radius: 10)
[01:31:09 -136151.113656] SLOW spr round 9 (radius: 15)
[01:37:48 -136151.113655] SLOW spr round 10 (radius: 20)
[01:46:58 -136151.113655] SLOW spr round 11 (radius: 25)
[01:57:38 -136151.113655] Model parameter optimization (eps = 0.100000)

[01:57:55] [worker #0] ML tree search #1, logLikelihood: -136150.871605

[01:57:55 -489187.282116] Initial branch length optimization
[01:58:02] [worker #2] ML tree search #3, logLikelihood: -136144.825474
[01:58:03 -423893.051970] Model parameter optimization (eps = 10.000000)
[01:58:56 -421792.831517] AUTODETECT spr round 1 (radius: 5)
[01:59:53] [worker #4] ML tree search #5, logLikelihood: -136144.075964
[02:03:27 -278045.714723] AUTODETECT spr round 2 (radius: 10)
[02:07:29] [worker #5] ML tree search #6, logLikelihood: -136141.835353
[02:08:32 -202148.593250] AUTODETECT spr round 3 (radius: 15)
[02:09:33] [worker #3] ML tree search #4, logLikelihood: -136131.534342
[02:13:41 -173095.977465] AUTODETECT spr round 4 (radius: 20)
[02:19:56 -160082.354140] AUTODETECT spr round 5 (radius: 25)
[02:27:17 -158477.260497] SPR radius for FAST iterations: 25 (autodetect)
[02:27:17 -158477.260497] Model parameter optimization (eps = 3.000000)
[02:27:26 -158475.241431] FAST spr round 1 (radius: 25)
[02:28:20] [worker #1] ML tree search #2, logLikelihood: -136175.337873
[02:33:08 -137064.039586] FAST spr round 2 (radius: 25)
[02:37:15 -136361.733199] FAST spr round 3 (radius: 25)
[02:41:03 -136235.849867] FAST spr round 4 (radius: 25)
[02:44:12 -136220.831540] FAST spr round 5 (radius: 25)
[02:47:04 -136220.545946] FAST spr round 6 (radius: 25)
[02:49:42 -136220.545750] Model parameter optimization (eps = 1.000000)
[02:50:05 -136196.702371] SLOW spr round 1 (radius: 5)
[02:54:20 -136141.912296] SLOW spr round 2 (radius: 5)
[02:58:30 -136124.644891] SLOW spr round 3 (radius: 5)
[03:02:39 -136123.989256] SLOW spr round 4 (radius: 5)
[03:06:42 -136123.093080] SLOW spr round 5 (radius: 5)
[03:11:11 -136123.093052] SLOW spr round 6 (radius: 10)
[03:15:26 -136122.019873] SLOW spr round 7 (radius: 5)
[03:20:36 -136122.019873] SLOW spr round 8 (radius: 10)
[03:25:23 -136122.019872] SLOW spr round 9 (radius: 15)
[03:31:51 -136122.019872] SLOW spr round 10 (radius: 20)
[03:40:50 -136122.019871] SLOW spr round 11 (radius: 25)
[03:44:05] [worker #3] ML tree search #10, logLikelihood: -136155.978127
[03:52:10 -136122.019871] Model parameter optimization (eps = 0.100000)

[03:52:28] [worker #0] ML tree search #7, logLikelihood: -136120.686820

[03:52:28 -488896.074344] Initial branch length optimization
[03:52:36 -422742.222965] Model parameter optimization (eps = 10.000000)
[03:53:33 -420646.822097] AUTODETECT spr round 1 (radius: 5)
[03:54:10] [worker #4] ML tree search #11, logLikelihood: -136121.661303
[03:55:22] [worker #2] ML tree search #9, logLikelihood: -136138.369106
[03:58:36 -276598.097208] AUTODETECT spr round 2 (radius: 10)
[04:02:44] [worker #5] ML tree search #12, logLikelihood: -136151.355676
[04:03:48 -205527.565079] AUTODETECT spr round 3 (radius: 15)
[04:09:32 -172291.100721] AUTODETECT spr round 4 (radius: 20)
[04:15:41 -158754.437520] AUTODETECT spr round 5 (radius: 25)
[04:23:37 -157601.451020] SPR radius for FAST iterations: 25 (autodetect)
[04:23:37 -157601.451020] Model parameter optimization (eps = 3.000000)
[04:24:06 -157566.917729] FAST spr round 1 (radius: 25)
[04:30:13 -137159.231371] FAST spr round 2 (radius: 25)
[04:34:48 -136271.870042] FAST spr round 3 (radius: 25)
[04:38:24 -136214.489311] FAST spr round 4 (radius: 25)
[04:41:36 -136214.488986] Model parameter optimization (eps = 1.000000)
[04:41:57 -136212.091609] SLOW spr round 1 (radius: 5)
[04:46:49 -136165.074302] SLOW spr round 2 (radius: 5)
[04:51:37 -136155.562301] SLOW spr round 3 (radius: 5)
[04:56:12 -136148.945405] SLOW spr round 4 (radius: 5)
[05:00:09 -136148.945325] SLOW spr round 5 (radius: 10)
[05:04:11 -136148.945309] SLOW spr round 6 (radius: 15)
[05:09:42] [worker #1] ML tree search #8, logLikelihood: -136137.778836
[05:11:25 -136147.871710] SLOW spr round 7 (radius: 5)
[05:17:02 -136147.871710] SLOW spr round 8 (radius: 10)
[05:22:01 -136147.871710] SLOW spr round 9 (radius: 15)
[05:29:00 -136147.871710] SLOW spr round 10 (radius: 20)
[05:38:17 -136147.871709] SLOW spr round 11 (radius: 25)
[05:42:24] [worker #3] ML tree search #16, logLikelihood: -136144.084998
[05:43:56] [worker #4] ML tree search #17, logLikelihood: -136130.153294
[05:50:20 -136147.871709] Model parameter optimization (eps = 0.100000)

[05:50:35] [worker #0] ML tree search #13, logLikelihood: -136147.711421

[05:50:35 -488485.558691] Initial branch length optimization
[05:50:44 -421355.848895] Model parameter optimization (eps = 10.000000)
[05:51:48 -419063.682764] AUTODETECT spr round 1 (radius: 5)
[05:52:11] [worker #2] ML tree search #15, logLikelihood: -136116.431109
[05:57:08 -277283.019744] AUTODETECT spr round 2 (radius: 10)
[06:01:58] [worker #5] ML tree search #18, logLikelihood: -136129.651942
[06:02:29 -205855.559085] AUTODETECT spr round 3 (radius: 15)
[06:07:39 -174261.814193] AUTODETECT spr round 4 (radius: 20)
[06:13:33 -161170.049810] AUTODETECT spr round 5 (radius: 25)
[06:20:47 -157589.204974] SPR radius for FAST iterations: 25 (autodetect)
[06:20:47 -157589.204974] Model parameter optimization (eps = 3.000000)
[06:21:15 -157568.171290] FAST spr round 1 (radius: 25)
[06:26:43 -137289.531912] FAST spr round 2 (radius: 25)
[06:31:33 -136309.593561] FAST spr round 3 (radius: 25)
[06:35:03 -136205.074458] FAST spr round 4 (radius: 25)
[06:38:08 -136192.649140] FAST spr round 5 (radius: 25)
[06:41:02 -136192.648895] Model parameter optimization (eps = 1.000000)
[06:41:21 -136191.511797] SLOW spr round 1 (radius: 5)
[06:46:00 -136129.930925] SLOW spr round 2 (radius: 5)
[06:50:19 -136128.117475] SLOW spr round 3 (radius: 5)
[06:54:24 -136128.117460] SLOW spr round 4 (radius: 10)
[06:58:27 -136128.117446] SLOW spr round 5 (radius: 15)
[07:05:48 -136127.029013] SLOW spr round 6 (radius: 5)
[07:11:08 -136127.029000] SLOW spr round 7 (radius: 10)
[07:12:28] [worker #1] ML tree search #14, logLikelihood: -136174.560701
[07:15:57 -136127.028988] SLOW spr round 8 (radius: 15)
[07:23:52 -136127.028975] SLOW spr round 9 (radius: 20)
[07:33:01 -136127.028964] SLOW spr round 10 (radius: 25)
[07:44:42 -136127.028952] Model parameter optimization (eps = 0.100000)

[07:44:51] [worker #0] ML tree search #19, logLikelihood: -136126.970470

[09:13:54] [worker #1] ML tree search #20, logLikelihood: -136140.829851

Optimized model parameters:

   Partition 0: noname
   Rate heterogeneity: FREE (4 cats, mean),  weights&rates: (0.243626,0.335072) (0.247346,0.402224) (0.245788,0.976850) (0.263240,2.198681) 
   Base frequencies (model): 
M0: 0.147383 0.017579 0.058208 0.017707 0.026331 0.041582 0.017494 0.027859 0.011849 0.076971 0.147823 0.019535 0.037132 0.029940 0.008059 0.088179 0.089653 0.006477 0.032308 0.097931 
M1: 0.063139 0.066357 0.011586 0.066571 0.010800 0.009276 0.053984 0.146986 0.034214 0.088822 0.098196 0.032390 0.021263 0.072697 0.016761 0.020711 0.020797 0.025463 0.045615 0.094372 
M2: 0.062457 0.066826 0.049332 0.065270 0.006513 0.041231 0.058965 0.080852 0.028024 0.037024 0.075925 0.064131 0.019620 0.028710 0.104579 0.056388 0.062027 0.008241 0.033124 0.050760 
M3: 0.106471 0.074171 0.044513 0.096390 0.002148 0.066733 0.158908 0.037625 0.020691 0.014608 0.028797 0.105352 0.007864 0.007477 0.083595 0.055726 0.047711 0.003975 0.010088 0.027159 
   Substitution rates (model): 
M 0: 0.295719 0.067388 0.253712 1.029289 0.107964 0.514644 10.868848 0.380498 0.084223 0.086976 0.188789 0.286389 0.155567 1.671061 2.132922 0.529591 0.115551 0.102453 0.916683 0.448317 0.457483 0.576016 1.741924 0.736017 0.704334 5.658311 0.123387 0.221777 93.433377 0.382175 0.235965 6.535048 0.525521 0.303537 0.641259 0.289466 0.102065 2.358429 0.251987 0.216561 0.503084 0.435271 4.873453 0.090748 0.033310 0.746537 0.128905 0.127321 0.904011 0.939733 0.435450 0.046646 0.262076 0.043986 0.189008 0.599450 109.901504 1.070052 5.229858 0.052764 0.021407 0.621146 0.081091 0.205164 5.164456 0.747330 0.308078 0.260889 0.185083 0.080708 0.029955 0.084794 1.862626 0.553477 0.151733 0.230320 0.096955 0.352526 0.590018 0.386853 1.559564 0.606648 0.587531 0.592318 0.885230 4.117654 0.246260 6.508329 0.054187 0.195703 1.669092 0.810168 0.066081 2.437439 0.165666 0.106333 0.093417 0.035149 0.072549 1.202023 1.634845 0.060194 0.069359 2.448827 0.232297 0.064822 3.537387 0.435384 0.290413 0.280695 0.105999 0.206603 0.404968 0.048984 0.069963 0.256662 0.228519 0.241077 4.320442 3.656545 0.290216 0.307466 0.096556 0.306067 0.204296 0.504221 1.991533 0.655465 6.799829 11.291065 0.961142 0.448965 6.227274 20.304886 0.205944 1.495537 0.091940 1.994320 0.754940 0.170343 0.050315 0.372166 0.206332 0.097050 5.381403 0.122332 3.256485 2.261319 0.848067 0.064441 0.102493 0.459041 0.133091 0.561215 0.457430 0.163849 5.260446 0.360946 0.389413 0.033291 0.115301 0.112593 1.559944 0.426508 0.132547 0.498634 0.559069 0.264728 0.693307 0.438856 0.306683 0.109129 18.392863 66.647302 0.400021 4.586081 2.099355 0.411347 0.476350 0.584622 3.634276 0.101797 0.148995 0.089177 0.034710 0.063603 0.755865 20.561407 0.133790 0.154902 
M 1: 0.066142 0.590377 0.069930 9.850951 1.101363 0.150375 0.568586 0.051668 0.127170 0.292429 0.071458 1.218562 0.075144 7.169085 30.139501 13.461692 0.021372 0.045779 4.270235 0.468325 0.013688 0.302287 1.353957 0.028386 0.037750 0.262130 0.016923 0.064289 0.855973 0.079621 0.011169 0.161937 0.276530 0.161053 0.081472 0.036742 0.030342 2.851667 3.932151 8.159169 0.219934 0.421974 2.468752 0.344765 0.210724 1.172204 0.763553 0.082464 0.726566 11.149790 4.782635 0.058046 0.498072 0.258487 0.146882 0.249672 0.560142 0.046719 0.106259 0.003656 0.004200 0.014189 0.009876 0.002656 0.040244 0.267322 0.053740 0.006597 0.027639 0.012745 0.582670 0.005035 0.275844 0.098208 0.445038 1.217010 0.033969 1.988516 0.681161 0.825960 18.762977 11.949233 0.286794 0.534219 4.336817 3.054085 0.129551 4.210126 0.165753 1.088704 1.889645 3.344809 0.111063 2.067758 3.547017 2.466507 0.188236 0.203493 0.281953 0.037250 0.029788 0.008541 0.014768 0.125869 0.056702 0.004186 0.110993 0.201148 0.139705 0.009201 0.012095 0.043812 0.013513 0.002533 0.005848 0.031390 0.021612 0.004854 0.129497 0.976631 0.053397 0.019475 0.004964 0.015539 0.031779 0.064558 0.065585 0.079927 0.095591 0.196886 0.408834 0.126088 0.037226 0.452302 0.016212 7.278994 0.029917 7.918203 0.450964 0.169797 0.104288 1.578530 0.015909 0.094365 16.179952 0.042762 14.799537 1.506485 0.637893 0.123793 0.641351 0.154810 0.140750 3.416059 0.259400 0.009457 0.090576 0.292108 0.297913 0.017172 0.021976 0.032578 1.375871 0.457399 0.598048 4.418398 0.239749 0.168432 2.950318 0.143327 0.328689 0.125011 0.562720 1.414883 0.227807 3.478333 2.984862 0.061299 0.077470 1.050562 13.974326 0.154326 0.224675 0.112000 0.060703 0.123480 5.294490 0.447011 0.033381 0.045528 
M 2: 0.733336 0.558955 0.503360 4.149599 1.415369 1.367574 1.263002 0.994098 0.517204 0.775054 0.763094 1.890137 0.540460 0.200122 4.972745 1.825593 0.450842 0.526135 3.839269 0.597671 0.058964 2.863355 2.872594 0.258365 0.366868 2.578946 0.358350 0.672023 5.349861 0.691594 0.063347 0.032875 0.821562 0.580847 0.661866 0.265730 0.395134 5.581680 1.279881 1.335650 0.397108 1.840061 5.739035 0.284730 0.109781 1.612642 0.466979 0.141582 0.019509 4.670980 1.967383 0.088064 0.581928 0.145401 0.225860 0.434096 2.292917 1.024707 0.821921 0.027824 0.021443 0.088850 0.060820 0.018288 0.042687 1.199607 0.420710 0.037642 0.141233 0.090101 1.043232 0.209978 0.823594 3.039380 1.463390 1.983693 0.397640 2.831098 4.102068 0.059723 5.901348 2.034980 2.600668 5.413080 4.193725 4.534772 0.377181 4.877840 0.370939 1.298542 3.509873 2.646440 0.087872 0.072299 1.139018 0.864479 0.390688 0.322761 0.625409 0.496780 0.532488 0.232460 0.169219 0.755219 0.379926 0.020447 0.023282 0.503875 0.577513 0.109318 0.153776 0.696533 0.398817 0.008940 0.043707 0.436013 0.087640 0.064863 0.036426 1.673207 0.124068 0.218118 0.039217 0.104335 0.349195 0.838324 0.888693 0.488389 1.385133 0.050226 0.962470 0.502294 1.065585 8.351808 0.377304 5.102837 0.561690 7.010411 3.054968 0.039318 0.204155 2.653232 0.564368 0.854294 15.559906 0.401070 8.929538 5.525874 0.067505 0.273372 0.437116 1.927515 0.940458 2.508169 1.357738 0.043394 0.023126 0.567639 1.048288 0.120994 0.180650 0.449074 3.135353 0.012695 0.570771 2.319555 1.856122 0.975427 3.404087 0.015631 0.458799 0.151684 4.154750 11.429924 1.457957 0.233109 0.077004 0.011074 0.026268 0.052132 8.113282 0.377578 0.429221 0.260296 0.222293 0.273138 2.903836 4.731579 0.564762 0.681215 
M 3: 0.658412 0.566269 0.854111 0.884454 1.309554 1.272639 1.874713 0.552007 0.227683 0.581512 0.695190 0.967985 0.344015 0.978992 3.427163 2.333253 0.154701 0.221089 2.088785 0.540749 0.058015 5.851132 2.294145 0.182966 0.684164 3.192521 0.528161 1.128882 3.010922 1.012866 0.227296 0.156635 0.878405 0.802754 0.830884 0.431617 0.456530 3.060574 1.279257 1.438430 0.431464 2.075952 4.840271 0.644656 0.266076 2.084975 0.720060 0.291854 0.028961 4.071574 2.258357 0.073037 1.238426 0.199728 0.160296 0.482619 2.992763 1.296206 0.841829 0.031467 0.048542 0.132774 0.133055 0.056045 0.209188 0.925172 0.360522 0.094591 0.313945 0.118104 0.992259 0.086318 2.149634 5.103188 3.775817 3.954021 0.190734 1.776095 4.495841 0.264277 7.063879 2.221150 3.017954 8.558815 4.310199 2.130054 0.571406 4.137385 0.437589 2.071689 2.498630 1.763546 0.116381 0.296578 1.033710 1.283423 0.312579 0.305772 0.681277 0.507160 0.351381 0.189152 0.217780 0.767361 0.278392 0.092075 0.177263 0.451893 0.653836 0.074620 0.181992 0.752277 0.679853 0.025780 0.082005 0.326441 0.343977 0.195877 0.217424 3.057583 0.377558 0.401252 0.072258 0.241015 0.665865 1.266791 0.680174 0.717301 4.001286 0.362942 1.189259 0.964545 1.350568 12.869737 0.531100 8.904999 0.652629 10.091413 2.671718 0.086367 0.359932 4.797423 0.336801 1.021885 23.029406 0.440178 14.013035 5.069337 0.539010 0.742569 0.780580 1.331875 1.531589 4.414850 1.082703 0.091278 0.172734 0.693405 1.422571 0.068958 0.163829 0.481711 4.643214 0.121821 0.584083 4.216178 1.677263 1.575754 5.046403 0.161015 1.531223 0.599244 5.832025 33.873091 1.914768 1.287474 0.444362 0.076328 0.079916 0.466823 5.231362 0.548763 0.831890 0.382271 0.208791 0.307846 3.717971 5.910440 0.282540 0.964421 


Final LogLikelihood: -136116.431109

AIC score: 276242.862217 / AICc score: 8320302.862217 / BIC score: 284078.568508
Free parameters (model + branch lengths): 2005

WARNING: Number of free parameters (K=2005) is larger than alignment size (n=368).
         This might lead to overfitting and compromise tree inference results!


WARNING: Best ML tree contains 1 near-zero branches!

Best ML tree with collapsed near-zero branches saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88.raxml.bestTreeCollapsed
Best ML tree saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88.raxml.bestTree
All ML trees saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88.raxml.mlTrees
Optimized model saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88.raxml.bestModel

Execution log saved to: /truba/home/emrah/WORKFOLDER/PROD/300621_run/phylogeny-snakemake/results/Q9UQ88/3_mltree/Q9UQ88.raxml.log

Analysis started: 05-Jul-2021 13:32:31 / finished: 05-Jul-2021 22:46:26

Elapsed time: 33235.293 seconds

Consumed energy: 2641.862 Wh (= 13 km in an electric car, or 66 km with an e-scooter!)